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Chaturvedi A, Sharma S, Shukla R. Drug Nanocrystals: A Delivery Channel for Antiviral Therapies. AAPS PharmSciTech 2024; 25:41. [PMID: 38366178 DOI: 10.1208/s12249-024-02754-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/23/2024] [Indexed: 02/18/2024] Open
Abstract
Viral infections represent a significant threat to global health due to their highly communicable and potentially lethal nature. Conventional antiviral interventions encounter challenges such as drug resistance, tolerability issues, specificity concerns, high costs, side effects, and the constant mutation of viral proteins. Consequently, the exploration of alternative approaches is imperative. Therefore, nanotechnology-embedded drugs excelled as a novel approach purporting severe life-threatening viral disease. Integrating nanomaterials and nanoparticles enables ensuring precise drug targeting, improved drug delivery, and fostered pharmacokinetic properties. Notably, nanocrystals (NCs) stand out as one of the most promising nanoformulations, offering remarkable characteristics in terms of physicochemical properties (higher drug loading, improved solubility, and drug retention), pharmacokinetics (enhanced bioavailability, dose reduction), and optical properties (light absorptivity, photoluminescence). These attributes make NCs effective in diagnosing and ameliorating viral infections. This review comprises the prevalence, pathophysiology, and resistance of viral infections along with emphasizing on failure of current antivirals in the management of the diseases. Moreover, the review also highlights the role of NCs in various viral infections in mitigating, diagnosing, and other NC-based strategies combating viral infections. In vitro, in vivo, and clinical studies evident for the effectiveness of NCs against viral pathogens are also discussed.
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Affiliation(s)
- Akanksha Chaturvedi
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER) - Raebareli, Lucknow, 226002, India
| | - Swapnil Sharma
- Department of Pharmacy, Banasthali University, Banasthali, Rajasthan, 304022, India
| | - Rahul Shukla
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER) - Raebareli, Lucknow, 226002, India.
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Gholipour S, Hosseini M, Nikaeen M, Hadi M, Sarmadi M, Saderi H, Hassanzadeh A. Quantification of human adenovirus in irrigation water-soil-crop continuum: are consumers of wastewater-irrigated vegetables at risk? ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:54561-54570. [PMID: 35304720 DOI: 10.1007/s11356-022-19588-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Because of health concerns regarding the presence of enteric viruses in wastewater effluents, this study was designed to investigate the occurrence of human adenovirus (HAdV) in the irrigation water-soil-crop continuum. Viral particles were extracted from wastewater and wastewater- or water-irrigated soil and crop samples and analyzed using real-time PCR. Concentration of fecal indicator bacteria (FIB) were also determined. Quantitative microbial risk assessment was performed to determine the HAdV illness risk associated with the consumption of wastewater-irrigated vegetables. HAdV-F was detected in 74% of wastewater effluent samples with a mean concentration of 38 Genomic Copy (GC)/mL. HAdV was also detected in wastewater-irrigated soil (2 × 102 GC/g) and crop (< 10 GC/g) samples, with no statistically significant difference in concentrations between wastewater- and freshwater-irrigated samples. The results showed no correlation between concentrations of FIB and HAdV in the analyzed samples. Mean probability of illness risk from consumption of wastewater-irrigated vegetables was 4 × 10-1 per person per year (pppy) which was about two orders of magnitude higher than the proposed value by WHO (10-3 pppy) for safe reuse of wastewater. This finding suggests that the wastewater reuse for irrigation of vegetables eaten raw could pose a threat to human health with respect to the risk of viral illness, signifying stricter management of wastewater reuse. However, because of uncertainties in the QMRA model, particularly the ratio of infectious to non-infectious virus particles, more data is required to validate the predicted risk. This information is especially important in arid and semi-arid regions where high temperatures, UV radiation intensity, and desiccation can efficiently inactivate microorganisms in the environment.
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Affiliation(s)
- Sahar Gholipour
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mona Hosseini
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mahnaz Nikaeen
- Department of Environmental Health Engineering, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran.
- Environment Research Center, Research Institute for Primordial Prevention of Non-Communicable Disease, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Mahdi Hadi
- Center for Water Quality Research (CWQR), Institute for Environmental Research (IER), Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdieh Sarmadi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Horieh Saderi
- Molecular Microbiology Research Center (MMRC), Shahed University, Tehran, Iran
| | - Akbar Hassanzadeh
- Department of Statistics & Epidemiology, School of Health, Isfahan University of Medical Sciences, Isfahan, Iran
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Augustine SAJ, Eason TN, Wade T, Griffin SM, Sams E, Simmons K, Ramudit M, Oshima K, Dufour A. Salivary Antibodies against Multiple Environmental Pathogens Found in Individuals Recreating at an Iowa Beach. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18115797. [PMID: 34071402 PMCID: PMC8199218 DOI: 10.3390/ijerph18115797] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 11/26/2022]
Abstract
Detecting environmental exposures and mitigating their impacts are growing global public health challenges. Antibody tests show great promise and have emerged as fundamental tools for large-scale exposure studies. Here, we apply, demonstrate and validate the utility of a salivary antibody multiplex immunoassay in measuring antibody prevalence and immunoconversions to six pathogens commonly found in the environment. The study aimed to assess waterborne infections in consenting beachgoers recreating at an Iowa riverine beach by measuring immunoglobulin G (IgG) antibodies against select pathogens in serially collected saliva samples. Results showed that nearly 80% of beachgoers had prior exposures to at least one of the targeted pathogens at the beginning of the study. Most of these exposures were to norovirus GI.1 (59.41%), norovirus GII.4 (58.79%) and Toxoplasma gondii (22.80%) and over half (56.28%) of beachgoers had evidence of previous exposure to multiple pathogens. Of individuals who returned samples for each collection period, 6.11% immunoconverted to one or more pathogens, largely to noroviruses (GI.1: 3.82% and GII.4: 2.29%) and T. gondii (1.53%). Outcomes of this effort illustrate that the multiplex immunoassay presented here serves as an effective tool for evaluating health risks by providing valuable information on the occurrence of known and emerging pathogens in population surveillance studies.
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Affiliation(s)
- Swinburne A. J. Augustine
- Center for Public Health and Environmental Assessment, United States Environmental Protection Agency, Cincinnati, OH 45268, USA;
- Correspondence: ; Tel.: +1-513-569-7132
| | - Tarsha N. Eason
- Center for Environmental Methods and Measurement, United States Environmental Protection Agency, Athens, GA 30605, USA;
| | - Tim Wade
- Center for Public Health and Environmental Assessment, United States Environmental Protection Agency, Research Triangle Park, NC 27709, USA; (T.W.); (E.S.)
| | - Shannon M. Griffin
- Center for Public Health and Environmental Assessment, United States Environmental Protection Agency, Cincinnati, OH 45268, USA;
| | - Elizabeth Sams
- Center for Public Health and Environmental Assessment, United States Environmental Protection Agency, Research Triangle Park, NC 27709, USA; (T.W.); (E.S.)
| | - Kaneatra Simmons
- Department of Arts and Sciences/Learning Support, Fort Valley State University, Fort Valley, GA 31030, USA;
| | - Malini Ramudit
- Oak Ridge Institute for Science Education, Oak Ridge, TN 37831, USA;
| | - Kevin Oshima
- Center for Environmental Methods and Measurement, United States Environmental Protection Agency, Cincinnati, OH 45268, USA; (K.O.); (A.D.)
| | - Alfred Dufour
- Center for Environmental Methods and Measurement, United States Environmental Protection Agency, Cincinnati, OH 45268, USA; (K.O.); (A.D.)
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Maus A, Strait L, Zhu D. Nanoparticles as delivery vehicles for antiviral therapeutic drugs. ENGINEERED REGENERATION 2021; 2:31-46. [PMID: 38620592 PMCID: PMC7988306 DOI: 10.1016/j.engreg.2021.03.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/11/2021] [Accepted: 03/09/2021] [Indexed: 02/08/2023] Open
Abstract
With the ongoing COVID-19 pandemic still escalating, many researchers are turning to nanotechnology as a method of treatment not only for this pandemic, but in preparation for the pandemics of the future. Given both a wide variety of biomaterials at their disposal and the recent rise of nanotechnology, scientists now have the means to release and distribute therapeutic drugs in a variety of ways. Such a variety permits medical professionals the ability to choose biomaterials and methods that would provide the best release and treatment methodologies for the viral ailment they are attempting to remedy. This integrative review discusses context of previous pandemics, viral pathogenesis, issues associated with the current state of antiviral delivery systems, numerous biomaterials used for this purpose, and further information regarding the ongoing global COVID-19 pandemic.
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Affiliation(s)
- Alexander Maus
- Department of Biomedical Engineering, Stony Brook University, United States
| | - Lia Strait
- Department of Biomedical Engineering, Stony Brook University, United States
| | - Donghui Zhu
- Department of Biomedical Engineering, Stony Brook University, United States
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Tumbo AM, Schindler T, Dangy JP, Orlova-Fink N, Bieri JR, Mpina M, Milando FA, Juma O, Hamad A, Nyakarungu E, Chemba M, Mtoro A, Ramadhan K, Olotu A, Makweba D, Mgaya S, Stuart K, Perreau M, Stapleton JT, Jongo S, Hoffman SL, Tanner M, Abdulla S, Daubenberger C. Role of human Pegivirus infections in whole Plasmodium falciparum sporozoite vaccination and controlled human malaria infection in African volunteers. Virol J 2021; 18:28. [PMID: 33499880 PMCID: PMC7837505 DOI: 10.1186/s12985-021-01500-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/20/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Diverse vaccination outcomes and protection levels among different populations pose a serious challenge to the development of an effective malaria vaccine. Co-infections are among many factors associated with immune dysfunction and sub-optimal vaccination outcomes. Chronic, asymptomatic viral infections can contribute to the modulation of vaccine efficacy through various mechanisms. Human Pegivirus-1 (HPgV-1) persists in immune cells thereby potentially modulating immune responses. We investigated whether Pegivirus infection influences vaccine-induced responses and protection in African volunteers undergoing whole P. falciparum sporozoites-based malaria vaccination and controlled human malaria infections (CHMI). METHODS HPgV-1 prevalence was quantified by RT-qPCR in plasma samples of 96 individuals before, post vaccination with PfSPZ Vaccine and after CHMI in cohorts from Tanzania and Equatorial Guinea. The impact of HPgV-1 infection was evaluated on (1) systemic cytokine and chemokine levels measured by Luminex, (2) PfCSP-specific antibody titers quantified by ELISA, (3) asexual blood-stage parasitemia pre-patent periods and parasite multiplication rates, (4) HPgV-1 RNA levels upon asexual blood-stage parasitemia induced by CHMI. RESULTS The prevalence of HPgV-1 was 29.2% (28/96) and sequence analysis of the 5' UTR and E2 regions revealed the predominance of genotypes 1, 2 and 5. HPgV-1 infection was associated with elevated systemic levels of IL-2 and IL-17A. Comparable vaccine-induced anti-PfCSP antibody titers, asexual blood-stage multiplication rates and pre-patent periods were observed in HPgV-1 positive and negative individuals. However, a tendency for higher protection levels was detected in the HPgV-1 positive group (62.5%) compared to the negative one (51.6%) following CHMI. HPgV-1 viremia levels were not significantly altered after CHMI. CONCLUSIONS HPgV-1 infection did not alter PfSPZ Vaccine elicited levels of PfCSP-specific antibody responses and parasite multiplication rates. Ongoing HPgV-1 infection appears to improve to some degree protection against CHMI in PfSPZ-vaccinated individuals. This is likely through modulation of immune system activation and systemic cytokines as higher levels of IL-2 and IL17A were observed in HPgV-1 infected individuals. CHMI is safe and well tolerated in HPgV-1 infected individuals. Identification of cell types and mechanisms of both silent and productive infection in individuals will help to unravel the biology of this widely present but largely under-researched virus.
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Affiliation(s)
- Anneth-Mwasi Tumbo
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Bagamoyo, Tanzania
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Socinstr. 57, 4002, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Tobias Schindler
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Socinstr. 57, 4002, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jean-Pierre Dangy
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Socinstr. 57, 4002, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Nina Orlova-Fink
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Socinstr. 57, 4002, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jose Raso Bieri
- Equatorial Guinea Malaria Vaccine Initiative, Malabo, Bioko Norte, Equatorial Guinea
| | - Maximillian Mpina
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Bagamoyo, Tanzania
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Socinstr. 57, 4002, Basel, Switzerland
- University of Basel, Basel, Switzerland
- Equatorial Guinea Malaria Vaccine Initiative, Malabo, Bioko Norte, Equatorial Guinea
| | - Florence A Milando
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Bagamoyo, Tanzania
| | - Omar Juma
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Bagamoyo, Tanzania
| | - Ali Hamad
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Bagamoyo, Tanzania
- Equatorial Guinea Malaria Vaccine Initiative, Malabo, Bioko Norte, Equatorial Guinea
| | - Elizabeth Nyakarungu
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Bagamoyo, Tanzania
- Equatorial Guinea Malaria Vaccine Initiative, Malabo, Bioko Norte, Equatorial Guinea
| | - Mwajuma Chemba
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Bagamoyo, Tanzania
- Equatorial Guinea Malaria Vaccine Initiative, Malabo, Bioko Norte, Equatorial Guinea
| | - Ali Mtoro
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Bagamoyo, Tanzania
- Equatorial Guinea Malaria Vaccine Initiative, Malabo, Bioko Norte, Equatorial Guinea
| | - Kamaka Ramadhan
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Bagamoyo, Tanzania
- Equatorial Guinea Malaria Vaccine Initiative, Malabo, Bioko Norte, Equatorial Guinea
| | - Ally Olotu
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Bagamoyo, Tanzania
- Equatorial Guinea Malaria Vaccine Initiative, Malabo, Bioko Norte, Equatorial Guinea
| | - Damas Makweba
- Dar-Es-Salaam Institute of Technology, Dar-Es-Salaam, Tanzania
- Tanzania Education and Research Networks, Dar-Es-Salaam, Tanzania
- Tanzania Commission for Science and Technology, Dar-Es-Salaam, Tanzania
| | - Stephen Mgaya
- Tanzania Education and Research Networks, Dar-Es-Salaam, Tanzania
- Tanzania Commission for Science and Technology, Dar-Es-Salaam, Tanzania
| | - Kenneth Stuart
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, 307 Westlake Avenue, N. Suite 500, Seattle, WA, 98109, USA
| | | | - Jack T Stapleton
- Iowa City Veterans Administration and the University of Iowa, 200 Hawkins Drive, Iowa City, IA, 52242, USA
| | - Said Jongo
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Bagamoyo, Tanzania
- Equatorial Guinea Malaria Vaccine Initiative, Malabo, Bioko Norte, Equatorial Guinea
| | | | - Marcel Tanner
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Socinstr. 57, 4002, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Salim Abdulla
- Department of Intervention and Clinical Trials, Ifakara Health Institute, Bagamoyo, Tanzania
- Equatorial Guinea Malaria Vaccine Initiative, Malabo, Bioko Norte, Equatorial Guinea
| | - Claudia Daubenberger
- Department of Medical Parasitology and Infection Biology, Clinical Immunology Unit, Swiss Tropical and Public Health Institute, Socinstr. 57, 4002, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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Paskey AC, Ng JHJ, Rice GK, Chia WN, Philipson CW, Foo RJH, Cer RZ, Long KA, Lueder MR, Frey KG, Hamilton T, Mendenhall IH, Smith GJ, Wang LF, Bishop-Lilly KA. The temporal RNA virome patterns of a lesser dawn bat ( Eonycteris spelaea) colony revealed by deep sequencing. Virus Evol 2020; 6:veaa017. [PMID: 33747541 PMCID: PMC7079719 DOI: 10.1093/ve/veaa017] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The virosphere is largely unexplored and the majority of viruses are yet to be represented in public sequence databases. Bats are rich reservoirs of viruses, including several zoonoses. In this study, high throughput sequencing (HTS) of viral RNA extracted from swabs of four body sites per bat per timepoint is used to characterize the virome through a longitudinal study of a captive colony of fruit nectar bats, species Eonycteris spelaea in Singapore. Through unbiased shotgun and target enrichment sequencing, we identify both known and previously unknown viruses of zoonotic relevance and define the population persistence and temporal patterns of viruses from families that have the capacity to jump the species barrier. To our knowledge, this is the first study that combines probe-based viral enrichment with HTS to create a viral profile from multiple swab sites on individual bats and their cohort. This work demonstrates temporal patterns of the lesser dawn bat virome, including several novel viruses. Given the known risk for bat-human zoonoses, a more complete understanding of the viral dynamics in South-eastern Asian bats has significant implications for disease prevention and control. The findings of this study will be of interest to U.S. Department of Defense personnel stationed in the Asia-Pacific region and regional public health laboratories engaged in emerging infectious disease surveillance efforts.
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Affiliation(s)
- Adrian C Paskey
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd, Bethesda, MD 20814, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Justin H J Ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Gregory K Rice
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Wan Ni Chia
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Casandra W Philipson
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Defense Threat Reduction Agency, 8725 John J. Kingman Rd., Fort Belvoir, VA 22060, USA
| | - Randy J H Foo
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Regina Z Cer
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Kyle A Long
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Matthew R Lueder
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
- Leidos, 11951 Freedom Dr., Reston, VA 20190, USA
| | - Kenneth G Frey
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
| | - Theron Hamilton
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
| | - Ian H Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Gavin J Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Lin-Fa Wang
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, 8 College Road, Singapore 169857
| | - Kimberly A Bishop-Lilly
- Department of Microbiology and Immunology, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Rd, Bethesda, MD 20814, USA
- Genomics and Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center – Frederick, 8400 Research Plaza, Fort Detrick, MD 21702, USA
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Gu W, Miller S, Chiu CY. Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2018; 14:319-338. [PMID: 30355154 DOI: 10.1146/annurev-pathmechdis-012418-012751] [Citation(s) in RCA: 735] [Impact Index Per Article: 122.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nearly all infectious agents contain DNA or RNA genomes, making sequencing an attractive approach for pathogen detection. The cost of high-throughput or next-generation sequencing has been reduced by several orders of magnitude since its advent in 2004, and it has emerged as an enabling technological platform for the detection and taxonomic characterization of microorganisms in clinical samples from patients. This review focuses on the application of untargeted metagenomic next-generation sequencing to the clinical diagnosis of infectious diseases, particularly in areas in which conventional diagnostic approaches have limitations. The review covers ( a) next-generation sequencing technologies and common platforms, ( b) next-generation sequencing assay workflows in the clinical microbiology laboratory, ( c) bioinformatics analysis of metagenomic next-generation sequencing data, ( d) validation and use of metagenomic next-generation sequencing for diagnosing infectious diseases, and ( e) significant case reports and studies in this area. Next-generation sequencing is a new technology that has the promise to enhance our ability to diagnose, interrogate, and track infectious diseases.
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Affiliation(s)
- Wei Gu
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA;
| | - Steve Miller
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA;
| | - Charles Y Chiu
- Department of Laboratory Medicine, University of California, San Francisco, California 94107, USA; .,Department of Medicine, Division of Infectious Diseases, University of California, San Francisco, California 94107, USA
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Hasche D, Vinzón SE, Rösl F. Cutaneous Papillomaviruses and Non-melanoma Skin Cancer: Causal Agents or Innocent Bystanders? Front Microbiol 2018; 9:874. [PMID: 29770129 PMCID: PMC5942179 DOI: 10.3389/fmicb.2018.00874] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 04/16/2018] [Indexed: 12/12/2022] Open
Abstract
There is still controversy in the scientific field about whether certain types of cutaneous human papillomaviruses (HPVs) are causally involved in the development of non-melanoma skin cancer (NMSC). Deciphering the etiological role of cutaneous HPVs requires - besides tissue culture systems - appropriate preclinical models to match the obtained results with clinical data from affected patients. Clear scientific evidence about the etiology and underlying mechanisms involved in NMSC development is fundamental to provide reasonable arguments for public health institutions to classify at least certain cutaneous HPVs as group 1 carcinogens. This in turn would have implications on fundraising institutions and health care decision makers to force - similarly as for anogenital cancer - the implementation of a broad vaccination program against "high-risk" cutaneous HPVs to prevent NMSC as the most frequent cancer worldwide. Precise knowledge of the multi-step progression from normal cells to cancer is a prerequisite to understand the functional and clinical impact of cofactors that affect the individual outcome and the personalized treatment of a disease. This overview summarizes not only recent arguments that favor the acceptance of a viral etiology in NMSC development but also reflects aspects of causality in medicine, the use of empirically meaningful model systems and strategies for prevention.
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Affiliation(s)
- Daniel Hasche
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center, Heidelberg, Germany
| | - Sabrina E Vinzón
- Laboratory of Molecular and Cellular Therapy, Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
| | - Frank Rösl
- Division of Viral Transformation Mechanisms, Research Program "Infection, Inflammation and Cancer", German Cancer Research Center, Heidelberg, Germany
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9
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Antonelli G, Cutler S. Evolution of the Koch postulates: towards a 21st-century understanding of microbial infection. Clin Microbiol Infect 2016; 22:583-4. [PMID: 27064135 DOI: 10.1016/j.cmi.2016.03.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 03/29/2016] [Indexed: 12/17/2022]
Affiliation(s)
- G Antonelli
- Department of Molecular Medicine and Pasteur Institute, Cenci Bolognetti Foundation, 'Sapienza' University of Rome, Italy
| | - S Cutler
- School of Health, Sport and Bioscience, University of East London, London, UK.
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